Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019575.1 Corchorus olitorius cultivar O-4 contig19608, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25913
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:14 original size:2 final size:2
Alignment explanation
Indices: 8--79 Score: 126
Period size: 2 Copynumber: 36.0 Consensus size: 2
1 TCATCTA
8 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
50 CT CT CT CT CT AT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
80 TAATCATATG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:470 original size:1 final size:1
Alignment explanation
Indices: 464--490 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
454 ACTGTTATCG
464 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
491 GACATTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2275 original size:17 final size:17
Alignment explanation
Indices: 2253--2290 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2243 AGCAAGGCAG
2253 AAGCTTGCTACACTGTT
1 AAGCTTGCTACACTGTT
2270 AAGCTTGCTACACTGTT
1 AAGCTTGCTACACTGTT
2287 AAGC
1 AAGC
2291 AGCAGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (17 bp):
AAGCTTGCTACACTGTT
Found at i:2448 original size:13 final size:14
Alignment explanation
Indices: 2432--2463 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2422 CCAAAACAGA
2432 GAGAAGAAA-CAAT
1 GAGAAGAAATCAAT
2445 GAGAAGAAATCAAT
1 GAGAAGAAATCAAT
2459 G-GAAG
1 GAGAAG
2464 GGGATGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (14 bp):
GAGAAGAAATCAAT
Found at i:4594 original size:23 final size:22
Alignment explanation
Indices: 4544--4597 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
4534 GGTGGCAAAA
4544 TGAACCCGACCCCAGAAAAACC
1 TGAACCCGACCCCAGAAAAACC
* *
4566 TGAACCCGACCCGAGAAAAATC
1 TGAACCCGACCCCAGAAAAACC
4588 TGAAACCCGA
1 TG-AACCCGA
4598 TTGTAGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.41, C:0.35, G:0.17, T:0.07
Consensus pattern (22 bp):
TGAACCCGACCCCAGAAAAACC
Found at i:7816 original size:14 final size:14
Alignment explanation
Indices: 7797--7837 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
7787 GGCCTGTAAA
7797 GTAATTTATGTTAG
1 GTAATTTATGTTAG
7811 GTAATTTATGTTAG
1 GTAATTTATGTTAG
7825 GTAATTTATGTTA
1 GTAATTTATGTTA
7838 TTAAGTTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (14 bp):
GTAATTTATGTTAG
Found at i:8524 original size:67 final size:67
Alignment explanation
Indices: 8439--9010 Score: 601
Period size: 67 Copynumber: 8.6 Consensus size: 67
8429 AGTAAAGATT
* * * *
8439 TATTTTCTCTTTCCAAAAATACCCTTTCGGTTGAAGGGTCAGTTTCGTCTTTTTACGTCCAAGTT
1 TATTTTC-ATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTT
8504 TAG
65 TAG
* *
8507 TATTTTCATTTCCAAAAATACCCTTTCGATCGAAAGGTCAGTTTCGTCTTTTTACATTCAAGTTT
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTT
8572 AG
66 AG
* * * * *
8574 TATTTTCATTTCCGAAAATACCATTTCAGTCGAAGGGTCGGTTTTGTCTTTTTACATTCAAGTTT
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTT
8639 AG
66 AG
* *
8641 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTTAGTTTCGTCTTTTTACATTCAAGTTC
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTT
8706 AG
66 AG
* *
8708 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAATTTCGTCTTTTTGCATTC-AGATT
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAG-TT
8772 TAG
65 TAG
* * * * * * *
8775 T-TTTAC-TTTCCAAAAATACCCTTCCGGTCGAAGGGTCAGTTTCATCAAGATATTGCATTTAAG
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTC---TTTTTACATTCAAG
*
8838 TCTAG
63 TTTAG
* * * * * **
8843 T-CTTTC-TTTCCAAAGAATACCCTTTCGGTCAAAGGGTCAATTTCGTCATTCTTGCATTTGAGT
1 TATTTTCATTTCCAAA-AATACCCTTTCGGTCGAAGGGTCAGTTTCGTC-TTTTTACATTCAAGT
8906 TTA-
64 TTAG
* * * * **
8909 -CTTTTGATTTCCAAAAAATACCCTTTCGGT-GAAAAGGTCAGTTTCATCATTTCCACATTTC-A
1 TATTTTCATTTCC-AAAAATACCCTTTCGGTCG-AAGGGTCAGTTTCGTC-TTTTTACA-TTCAA
8971 GTTTA-
62 GTTTAG
* * * *
8976 T-TCTAC-TTTCCAAAAATGCCCTTTCGGTCAAAGGG
1 TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGG
9011 CGAGTTTTGT
Statistics
Matches: 431, Mismatches: 60, Indels: 29
0.83 0.12 0.06
Matches are distributed among these distances:
65 57 0.13
66 14 0.03
67 294 0.68
68 36 0.08
69 30 0.07
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (67 bp):
TATTTTCATTTCCAAAAATACCCTTTCGGTCGAAGGGTCAGTTTCGTCTTTTTACATTCAAGTTT
AG
Found at i:9618 original size:32 final size:32
Alignment explanation
Indices: 9539--9634 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 32
9529 ACTCAATCTA
* * * * *
9539 AACCCGAACTCGAATTAACCTGACTCAAAATT
1 AACCCGAACCCAAATCAACCTGACCCAAATTT
* *
9571 -GCCCGAACCCGAATCAACCTGACCCAAATTT
1 AACCCGAACCCAAATCAACCTGACCCAAATTT
* *
9602 AACCCGAACCTAAATCAATCC-GATCCAAATTT
1 AACCCGAACCCAAATCAA-CCTGACCCAAATTT
9634 A
1 A
9635 CCAAGCCTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 26 0.49
32 25 0.47
33 2 0.04
ACGTcount: A:0.39, C:0.32, G:0.09, T:0.20
Consensus pattern (32 bp):
AACCCGAACCCAAATCAACCTGACCCAAATTT
Found at i:13743 original size:17 final size:17
Alignment explanation
Indices: 13721--13754 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13711 GCTTAATGCC
13721 TTTTAAATAAGGATTCA
1 TTTTAAATAAGGATTCA
13738 TTTTAAATAAGGATTCA
1 TTTTAAATAAGGATTCA
13755 GATTCGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAATAAGGATTCA
Found at i:15073 original size:17 final size:17
Alignment explanation
Indices: 15048--15088 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
15038 ATTACCTCTC
* *
15048 AGATGACTGGTGATCTT
1 AGATTACTGGTAATCTT
15065 AGATTACTGGTAATCTT
1 AGATTACTGGTAATCTT
*
15082 ATATTAC
1 AGATTAC
15089 CTAGGTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (17 bp):
AGATTACTGGTAATCTT
Found at i:16006 original size:8 final size:8
Alignment explanation
Indices: 15995--16024 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
15985 AGGGTTTTTC
15995 TTTTTCTT
1 TTTTTCTT
16003 TTTTTCTTT
1 TTTTTC-TT
16012 TTTTTCTT
1 TTTTTCTT
16020 TTTTT
1 TTTTT
16025 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:16006 original size:14 final size:13
Alignment explanation
Indices: 15989--16027 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
15979 TATTTTAGGG
15989 TTTTTCTTTTTCTT
1 TTTTTCTTTTT-TT
16003 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
16016 TCTTTT-TTTTTT
1 T-TTTTCTTTTTT
16028 AAATTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:16026 original size:10 final size:9
Alignment explanation
Indices: 15995--16025 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
15985 AGGGTTTTTC
15995 TTTTTC-TT
1 TTTTTCTTT
16003 TTTTTCTTT
1 TTTTTCTTT
16012 TTTTTCTTT
1 TTTTTCTTT
16021 TTTTT
1 TTTTT
16026 TTAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:16075 original size:19 final size:19
Alignment explanation
Indices: 16051--16120 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
16041 ATTAGTTATT
16051 ATTATTTTATGATTAATTA
1 ATTATTTTATGATTAATTA
16070 ATTATTGATT-T-ATTAATTA
1 ATTATT--TTATGATTAATTA
** *
16089 ATTATTAAATTATT--TTA
1 ATTATTTTATGATTAATTA
*
16106 ATTATTGTATGATTA
1 ATTATTTTATGATTA
16121 TTTTAGGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 14 0.34
18 1 0.02
19 23 0.56
20 1 0.02
21 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTATTTTATGATTAATTA
Found at i:16093 original size:11 final size:11
Alignment explanation
Indices: 16030--16109 Score: 55
Period size: 11 Copynumber: 7.7 Consensus size: 11
16020 TTTTTTTTAA
*
16030 ATTAATTAATA
1 ATTAATTAATT
*
16041 ATTAGTT-ATT
1 ATTAATTAATT
* * *
16051 ATTATTTTATG
1 ATTAATTAATT
16062 ATTAATTAATT
1 ATTAATTAATT
*
16073 ATTGA-T--TT
1 ATTAATTAATT
16081 ATTAATTAATT
1 ATTAATTAATT
16092 ATTAAATT-ATT
1 ATT-AATTAATT
16103 -TTAATTA
1 ATTAATTA
16110 TTGTATGATT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
8 6 0.11
9 5 0.09
10 11 0.20
11 28 0.52
12 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:16139 original size:8 final size:8
Alignment explanation
Indices: 16063--16209 Score: 74
Period size: 8 Copynumber: 17.9 Consensus size: 8
16053 TATTTTATGA
*
16063 TTAATTAA
1 TTAATTAT
16071 TT-ATTGAT
1 TTAATT-AT
*
16079 TT-ATTAA
1 TTAATTAT
16086 TTAATTAT
1 TTAATTAT
*
16094 TAAATTATT
1 TTAATTA-T
16103 TTAATTAT
1 TTAATTAT
16111 TGTATGATTATT
1 T-TA--ATTA-T
**
16123 TTAGGTAT
1 TTAATTAT
16131 TTAATTAT
1 TTAATTAT
**
16139 TTAGCTAT
1 TTAATTAT
16147 TTGAATTATT
1 TT-AATTA-T
16157 TTATGATTAT
1 TTA--ATTAT
16167 TTAATTA-
1 TTAATTAT
16174 TTAATT-T
1 TTAATTAT
*
16181 ATTAATTAG
1 -TTAATTAT
16190 TT-ATTA-
1 TTAATTAT
16196 TT-ATTAT
1 TTAATTAT
16203 TTAATTA
1 TTAATTA
16210 GGTATTGGTG
Statistics
Matches: 109, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
6 6 0.06
7 18 0.17
8 51 0.47
9 15 0.14
10 7 0.06
11 10 0.09
12 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.59
Consensus pattern (8 bp):
TTAATTAT
Found at i:16172 original size:36 final size:36
Alignment explanation
Indices: 16128--16209 Score: 96
Period size: 36 Copynumber: 2.3 Consensus size: 36
16118 TTATTTTAGG
*
16128 TATTTAATTATTTAGCTATTTGAATTA-TT-TTATGAT
1 TATTTAATTATTAAGCTA-TT-AATTAGTTATTATGAT
** *
16164 TATTTAATTATTAATTTATTAATTAGTTATTATTAT
1 TATTTAATTATTAAGCTATTAATTAGTTATTATGAT
16200 TATTTAATTA
1 TATTTAATTA
16210 GGTATTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 5 0.12
35 4 0.10
36 31 0.77
ACGTcount: A:0.34, C:0.01, G:0.05, T:0.60
Consensus pattern (36 bp):
TATTTAATTATTAAGCTATTAATTAGTTATTATGAT
Found at i:17157 original size:33 final size:32
Alignment explanation
Indices: 17102--17163 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
17092 GAAGTTGAAA
17102 ACTTAGGAAGTTAGAAAGTGAGAGAATTTACT
1 ACTTAGGAAGTTAGAAAGTGAGAGAATTTACT
*
17134 ACTTTGGAAGTTTAG-AAGTTGAGAGAATTT
1 ACTTAGGAAG-TTAGAAAG-TGAGAGAATTT
17164 TGAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (32 bp):
ACTTAGGAAGTTAGAAAGTGAGAGAATTTACT
Found at i:18807 original size:114 final size:116
Alignment explanation
Indices: 18551--18816 Score: 403
Period size: 115 Copynumber: 2.3 Consensus size: 116
18541 AGAATTCAAC
* * *
18551 TCAAGTTTTATTATATTGTTATGAATGCTT-AGTTTTTTCTTTTTCTTTTTTTTTTCCAAACATG
1 TCAA-TTTTA-TATATTGTTATGAATG-TTCAGTTTTTTCTTTCTCCTTTTTATTTCCAAACATG
* * *
18615 AATTAATATTGTTATGAATGCTCAATTTTTTTTTCAGATAGTTTATTTTTTTTT
63 AATGAATATTGTTATGAATGCTCAAATTTTTTTCCAGATAGTTTATTTTTTTTT
*
18669 TCAATTTTATATATTGTTATGAATGTTCGGTTTTTTC-TTCTCCTTTTTATTTCCAAACATGAAT
1 TCAATTTTATATATTGTTATGAATGTTCAGTTTTTTCTTTCTCCTTTTTATTTCCAAACATGAAT
*
18733 GAATGTTGTTATGAATGCTCAAATTTTTTTCCAGATAGTTTA-TTTTTTTT
66 GAATATTGTTATGAATGCTCAAATTTTTTTCCAGATAGTTTATTTTTTTTT
*
18783 TCAATTTTATATATTGTTATGAATGCTCAGTTTT
1 TCAATTTTATATATTGTTATGAATGTTCAGTTTT
18817 ATTTTATTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
114 40 0.29
115 64 0.47
116 24 0.18
117 5 0.04
118 4 0.03
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.56
Consensus pattern (116 bp):
TCAATTTTATATATTGTTATGAATGTTCAGTTTTTTCTTTCTCCTTTTTATTTCCAAACATGAAT
GAATATTGTTATGAATGCTCAAATTTTTTTCCAGATAGTTTATTTTTTTTT
Found at i:25855 original size:2 final size:2
Alignment explanation
Indices: 25850--25912 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
25840 ATATATGTAT
25850 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25892 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
25913 T
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.